{ "type": "genome", "identifier": "GCA_003640285.1", "organism": "Lachnospiraceae bacterium", "title": "Lachnospiraceae bacterium", "description": "derived from metagenome; fragmented assembly; genus undefined", "data type": "Genome sequencing and assembly", "organization": "J. Craig Venter Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCA_003640285.1", "bioproject": "PRJNA383868", "biosample": "SAMN10134571", "wgs_master": "RBKB00000000.1", "refseq_category": "na", "taxid": "1898203", "species_taxid": "1898203", "organism_name": "Lachnospiraceae bacterium", "infraspecific_name": "", "isolate": "bin_21", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/12", "asm_name": "ASM364028v1", "submitter": "J. Craig Venter Institute", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/640/285/GCA_003640285.1_ASM364028v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-12", "dateModified": "2018-10-12", "datePublished": "2018-10-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Lachnospiraceae bacterium" ], "sample_taxid": [ "1898203" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Australia" ], "sample_host_location_id": [], "data_size": "2.990 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 97.92, "contamination": 245.36, "strain_heterogeneity": 25.11, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "10499032", "Number of Sequences": "2119", "Longest Sequences (bp)": "64950", "N50 (bp)": "5698", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.8", "Number of CDSs": "8003", "Average Protein Length": "307.5", "Coding Ratio (%)": "70.3", "Number of rRNAs": "0", "Number of tRNAs": "55", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lachnoanaerobaculum saburreum", "strain": "strain=DSM 3986", "accession": "GCA_000185385.1", "taxid": 467210, "species_taxid": 467210, "relation_to_type": "type", "validated": true, "ani": 94.5044, "matched_fragments": 760, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lachnoanaerobaculum gingivalis", "strain": "strain=KCOM 2030", "accession": "GCA_003862475.1", "taxid": 2490855, "species_taxid": 2490855, "relation_to_type": "type", "validated": true, "ani": 87.9635, "matched_fragments": 712, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lachnoanaerobaculum orale", "strain": "strain=DSM 24553", "accession": "GCA_003862485.1", "taxid": 979627, "species_taxid": 979627, "relation_to_type": "type", "validated": true, "ani": 85.9771, "matched_fragments": 675, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lachnoanaerobaculum umeaense", "strain": "strain=DSM 23576 = CCUG 58757", "accession": "GCA_003589745.1", "taxid": 617123, "species_taxid": 617123, "relation_to_type": "type", "validated": true, "ani": 83.8393, "matched_fragments": 656, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lachnoanaerobaculum umeaense", "strain": "strain=DSM 23576", "accession": "GCA_003254255.1", "taxid": 617123, "species_taxid": 617123, "relation_to_type": "type", "validated": true, "ani": 83.8024, "matched_fragments": 623, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Catonella morbi", "strain": "strain=ATCC 51271", "accession": "GCA_000160035.2", "taxid": 43997, "species_taxid": 43997, "relation_to_type": "type", "validated": true, "ani": 81.5548, "matched_fragments": 153, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Johnsonella ignava", "strain": "strain=ATCC 51276", "accession": "GCA_000235445.1", "taxid": 43995, "species_taxid": 43995, "relation_to_type": "type", "validated": true, "ani": 79.0654, "matched_fragments": 168, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Peptoanaerobacter stomatis", "strain": "strain=ACC19a", "accession": "GCA_000238115.1", "taxid": 796937, "species_taxid": 796937, "relation_to_type": "type", "validated": true, "ani": 79.0208, "matched_fragments": 83, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Catonella massiliensis", "strain": "strain=Marseille-Q4567", "accession": "GCA_016651435.1", "taxid": 2799636, "species_taxid": 2799636, "relation_to_type": "type", "validated": true, "ani": 78.6724, "matched_fragments": 93, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terrisporobacter glycolicus", "strain": "strain=DSM 1288", "accession": "GCA_000439105.1", "taxid": 36841, "species_taxid": 36841, "relation_to_type": "suspected-type", "validated": true, "ani": 74.7816, "matched_fragments": 52, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terrisporobacter glycolicus", "strain": "strain=ATCC 14880", "accession": "GCA_000373865.1", "taxid": 36841, "species_taxid": 36841, "relation_to_type": "suspected-type", "validated": true, "ani": 74.7384, "matched_fragments": 50, "total_fragments": 2356, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 97.92, "contamination": 245.36, "strain_heterogeneity": 25.11 }, "gtdb_result": [ { "accession": "GCA_900766185.1", "gtdb_species": "s__Johnsonella sp900766185", "ani": 95.8574, "matched_fragments": 491, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Johnsonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "97.99", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "inconclusive" }, { "accession": "GCA_000209465.1", "gtdb_species": "s__Lachnoanaerobaculum sp000209465", "ani": 95.2343, "matched_fragments": 796, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.01", "min_intra_species_ani": "98.01", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "inconclusive" }, { "accession": "GCF_000185385.1", "gtdb_species": "s__Lachnoanaerobaculum saburreum", "ani": 94.581, "matched_fragments": 757, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.52", "min_intra_species_ani": "97.46", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900167215.1", "gtdb_species": "s__Peptoanaerobacter yurii", "ani": 93.4739, "matched_fragments": 185, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Peptoanaerobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_905373785.1", "gtdb_species": "s__Johnsonella sp905373785", "ani": 92.9421, "matched_fragments": 387, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Johnsonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000296385.1", "gtdb_species": "s__Lachnoanaerobaculum sp000296385", "ani": 88.844, "matched_fragments": 709, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.95", "min_intra_species_ani": "96.95", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003862475.1", "gtdb_species": "s__Lachnoanaerobaculum gingivalis", "ani": 87.9402, "matched_fragments": 713, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000287675.1", "gtdb_species": "s__Lachnoanaerobaculum sp000287675", "ani": 87.671, "matched_fragments": 674, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.71", "min_intra_species_ani": "96.71", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_000146855.1", "gtdb_species": "s__Peptoanaerobacter margaretiae", "ani": 86.8893, "matched_fragments": 178, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Peptoanaerobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.24", "min_intra_species_ani": "97.24", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003862485.1", "gtdb_species": "s__Lachnoanaerobaculum orale", "ani": 85.96, "matched_fragments": 676, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.98", "min_intra_species_ani": "95.69", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.82", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003589745.1", "gtdb_species": "s__Lachnoanaerobaculum umeaense", "ani": 83.8333, "matched_fragments": 655, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000160035.2", "gtdb_species": "s__Catonella morbi", "ani": 81.5237, "matched_fragments": 154, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000235445.1", "gtdb_species": "s__Johnsonella ignava", "ani": 79.0654, "matched_fragments": 168, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Johnsonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000238115.1", "gtdb_species": "s__Peptoanaerobacter stomatis", "ani": 78.9659, "matched_fragments": 84, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Peptoanaerobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.77", "min_intra_species_ani": "95.04", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.83", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_016651435.1", "gtdb_species": "s__Catonella massiliensis", "ani": 78.6521, "matched_fragments": 94, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.56", "min_intra_species_ani": "95.38", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000439105.1", "gtdb_species": "s__Terrisporobacter glycolicus", "ani": 74.7816, "matched_fragments": 52, "total_fragments": 2356, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.67", "min_intra_species_ani": "99.35", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.239, "cell_length": 0.277, "doubling_h": 0.394, "growth_tmp": 37.0, "optimum_tmp": 36.16, "optimum_ph": 6.363, "genome_size": 3641163.5, "gc_content": 42.852, "coding_genes": 3283.347, "rRNA16S_genes": 6.0, "tRNA_genes": 63.727, "gram_stain": 0.885, "sporulation": 0.414, "motility": 0.448, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.988, "aerobic_respiration": 0.011, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.8, "coccus_cell_shape": 0.133, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.033, "vibrio_cell_shape": 0.033, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Lachnospirales", "f__Lachnospiraceae", "g__Johnsonella", "s__Johnsonella sp900766185" ], "_genome_taxon": [ "Lachnospiraceae", "bacterium", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Lachnospirales", "f__Lachnospiraceae", "g__Johnsonella", "s__Johnsonella sp900766185", "Bacteria", "Bacillota", "A", "Clostridia", "Lachnospirales", "Lachnospiraceae", "Johnsonella", "Johnsonella", "sp900766185" ], "_meo": [ { "id": "MEO_0000049", "label": "supragingival plaque" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }